ReviewRNA biology2013
Computational identification of functional RNA homologs in metagenomic data.
Review in RNA biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
25 citing papers in PubMed.
- From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid.BMC plant biology · 2025Article
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- High-Fat-Diet-Induced Oxidative Stress Linked to the Increased Colonization of Lactobacillus sakei in an Obese Population.Microbiology spectrum · 2021Article
- A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions.Bioinformatics (Oxford, England) · 2021Article
- Article
- A highly contiguous reference genome assembly for3 Biotech · 2021Article
- DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data.Frontiers in genetics · 2021Article
- Effects of Selenium- and Zinc-EnrichedAntioxidants (Basel, Switzerland) · 2020Article
- Article
- The locality dilemma of Sankoff-like RNA alignments.Bioinformatics (Oxford, England) · 2020Article
- Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria.Nature communications · 2020Article
- Article
- miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis.Briefings in bioinformatics · 2018Article
- Structural divergence creates new functional features in alphavirus genomes.Nucleic acids research · 2018Article
- Identification of Microbial Dark Matter in Antarctic Environments.Frontiers in microbiology · 2018Article
- Defining the SpeciesFrontiers in microbiology · 2018Article
- GLASSgo - Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence.Frontiers in genetics · 2018Article
- Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.Frontiers in genetics · 2017Review
- Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution.Wiley interdisciplinary reviews. RNA · 2017Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
A key step toward understanding a metagenomics data set is the identification of functional sequence elements within it, such as protein coding genes and structural RNAs. Relative to protein coding genes, structural RNAs are more difficult to identify because of their reduced alphabet size, lack of open reading frames, and short length. Infernal is a software package that implements "covariance models" (CMs) for RNA homology search, which harness both sequence and structural conservation when searching for RNA homologs. Thanks to the added statistical signal inherent in the secondary structure conservation of many RNA families, Infernal is more powerful than sequence-only based methods such as BLAST and profile HMMs. Together with the Rfam database of CMs, Infernal is a useful tool for identifying RNAs in metagenomics data sets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.